Determinants of Plant Species Richness along Elevational Gradients: Insights with Climate, Energy and Water-Energy Dynamics

Authors: Abhishek Kumar^#, Meenu Patil, Pardeep Kumar, Anand Narain Singh*
Affiliation: Soil Ecosystem and Restoration Ecology Lab, Department of Botany, Panjab University, Chandigarh 160014, India
*Corresponding author: dranand1212@gmail.com; ansingh@pu.ac.in
^#Maintainer: abhikumar.pu@gmail.com

Directory structure

. |- R |- 01_make-site-map.R |- 02_standardise-plant-names.R |- 03_get-elevation-ranges.R |- 04_calculate-richness.R |- 05_extract-explanatory-variables.R |- 06_compare-top-model.R |- calculate_band_area.R |- extract_climate.R |- data |- hkh |- chail_plants.csv |- chail.gpkg |- churdhar_plants.csv |- churdhar.gpkg |- ecs22945-sup-0004-datas1.csv |- khol_hi_raitan.gpkg |- morni_plants.csv |- morni.gpkg |- site_aet_cgiar.tif |- site_bio_chelsa.tif |- site_districts.gpkg |- site_evihomo_earthenv.tif |- site_npp_chelsa.tif |- site_pet_cgiar.tif |- site_soc_soilgrid.tif |- site_states.gpkg |- site_tri_earthenv.tif |- gv |- bmod_sem.gv |- hypothetical_sem.gv |- output |- 0417447-210914110416597.zip |- band_area.csv |- band_richness.csv |- chail_elev.tif |- churdhar_elev.tif |- morni_elev.tif |- site_elev.tif |- site_env.csv |- site_plants_wcvp.csv |- site_spec_elev.csv |- top_mod_comparison.csv |- apa7.csl |- credit_author.csv |- index.qmd |- README.md |- refs.bib |- richness-determinants.Rproj

Description of R scripts

| File name | Description |
|-----------|-------------| | 01_make-site-map.R | R codes to prepare the map for study sites (fig2_site-map.pdf) | | 02_standardise-plant-names.R | R codes to standardise botanical names according to WCVP (Govaerts et al., 2021). The standardised botanical names are saved as siteplantswcvp.csv | | 03_get-elevation-ranges.R | R codes to retrieve the species elevational ranges from published database (Rana & Rawat 2017, 2019) | | 04_calculate-richness.R | R codes with function used to calculate species richness from compiled dataset for each study site | | 05_extract-explanatory-variables.R | R codes to extract mean values of each explanatory variable for each site | | 06_compare-top-model.R | R codes to compare top models for each study site | | calculatebandarea.R | R codes for calculating the planar and slope-corrected area for each 100-m elevational band for each study site | | extract_climate.R | R script to extract climate data from WorldClim2 database (Fick & Hijmans 2017) and process to prepare Walter-Leith Diagrams for study sites |

Description of primary data files

| File name | Description |
|-----------|-------------| | hkh | Spatial boundary of Hindu Kush Himalayas (HKH) obtained from ICIMOD (2008) | | chail_plants.csv | Recorded plant species from literature survey for Chail Wildlife Sanctuary | | chail.gpkg | Digitised spatial boundary for Chail Wildlife Sanctuary | | churdhar_plants.csv | Recorded plant species from literature survey for Churdhar Wildlife Sanctuary | | churdhar.gpkg | Digitised spatial boundary for Churdhar Wildlife Sanctuary | | ecs22945-sup-0004-datas1.csv | Additional species distribution data from Rana, Price, & Qian (2019) | | kholhiraitan.gpkg | Digitised spatial boundary for Khol Hi Raitan Wildlife Sanctuary | | morni_plants.csv | Recorded plant species from literature survey for Morni Hills | | morni.gpkg | Digitised spatial boundary for Morni Hills | | siteaetcgiar.tif | Cropped actual evapotranspiration (AET) data obtained from Trabucco & Zomer (2019) | | sitebiochelsa.tif | Cropped bioclimatic variables data obtained from Karger et al. (2017) | | site_districts.gpkg | Spatial boundaries for Indian districts sharing the bounding box for selected study sites in the Himalayas | | siteevihomoearthenv.tif | Cropped EVI homogeneity index data obtained from Tuanmu & Jetz (2015) | | sitenppchelsa.tif | Cropped net primary productivity (NPP) data obtained from Karger et al. (2017) | | sitepetcgiar.tif | Cropped potential evapotranspiration (PET) data obtained from Zomer et al. (2022) | | sitesocsoilgrid.tif | Cropped soil organic carbon (SOC) data obtained from Hengl et al. (2017) | | site_states.gpkg | Spatial boundaries for north-western Indian States covering the study sites in the Western Himalayas | | sitetriearthenv.gpkg | Cropped terrain ruggedness index (TRI) data obtained from Amatulli et al. (2018) |

Description of Graphviz scripts

| File name | Description |
|-----------|-------------| | bmod_sem.gv | Graphviz script for final best path model for determinants of species richness | | hypothetical_sem.gv | Graphviz script for the priori hypothetical conceptual model for determinants of species richness |

Description of files derived using R

| File name | Description |
|-----------|-------------| | 0417447-210914110416597.zip | Species distribution dataset (Rana & Rawat 2017, 2019) downloaded from GBIF via rgbif package |
| band_area.csv | Calculated planar and slope-corrected area for each elevational band using the calculatebandarea.R script | | band_richness.csv | Estimated species richness for 100-m elevational bands for each site using the 04_calculate-richness.R script | | chail_elev.tif | Cropped elevation data for Chail WLS downloaded using the 05_extract-explanatory-variables.R script | | churdhar_elev.tif | Cropped elevation data for Churdhar WLS downloaded using the 05_extract-explanatory-variables.R script | | morni_elev.tif | Cropped elevation data for Morni Hills downloaded using the 05_extract-explanatory-variables.R script | | site_elev.tif | Cropped elevation data for study area downloaded using the 05_extract-explanatory-variables.R script | | site_env.tif | Prepared dataset with species richness and explanatory variables for each site processed using the 05_extract-explanatory-variables.R script | | siteplantswcvp.csv | Combined species check-list with botanical names standardised according to World Checklist of Vascular Plants (WCVP, Govaerts et al., 2021) using the 02_standardise-plant-names.R script | | sitespecelev.csv | Finally prepared dataset for standardised unique species and their elevational ranges for selected study sites using the 03_get-elevation-ranges.R script | | topmodcomparison.csv | Comparison of identified top model with previously proposed models of species richness using the 06_compare-top-model.R script |

Description of other files

| File name | Description |
|-----------|-------------| | apa7.csl | Citation Style Language (CSL) citation style for American Psychological Association (APA) 7th edition | | credit_author.csv | Documentation of each authors' contribution in CRediT (Contributor Roles Taxonomy) author statement | | index.qmd | Quarto markdown file with embedded R codes to reproduce the initial draft of manuscript | | refs.bib | Bibliographic entries for literature cited in the manuscript | | richness-determinants.Rproj | R project file |

Codebook for chail_plants.csv, chur_plants.csv and morni_plants.csv

| Column | Description | |-------------|-------------------------------------------------------------------| | givenname | Botanical name given in the published study | | powotaxa | Accepted botanical name by Plants of World Online (POWO) | | powoauthor | Accepted botanical name authorship by Plants of World Online (POWO) | | powodist | Distribution status (Introduced vs. Native) of plant according to Plants of World Online (POWO) |

All other columns refer to citation keys for studies identified through literature survey, i.e., Bhardwaj2017[^1], Champion1968[^2], eFI2022[^3], FOI2022[^4], Kumar2013[^5], Choudhary2007[^6], Choudhary2012[^7], Gupta1998[^8], Radha2019[^9], Subramani2014[^10], Thakur2021a[^11], Balkrishna2018a[^12], Balkrishna2018b[^13], Dhiman2020[^14], Dhiman2021[^15], Singh2014[^16]

Codebook for band_area.csv

| Column | Description | |-----------|-------------------------------------------------------------------| | elevation | Upper elevation of each 100-m elevational band in metres | | site | Name of site for which the MDE null model was run | | area2d | total planar area in km² for each elevational band | | area3d | total slope-corrected area in km² for each elevational band |

Codebook for band_richness.csv

| Column | Description | |-----------|-------------------------------------------------------------------| | elevation | Upper elevation of each 100-m elevational band in metres | | richness | Estimated species richness for each 100-m elevational band for selected sites | | site | Name of site for which the elevational species richness was estimated |

Codebook for site_env.csv

| Column | Description | |--------|-------------------------------------------------------------------| | site | Name of site for which the elevational species richness was estimated | | S | Estimated species richness for each 100-m elevational band for selected sites | | ELE | Upper elevation of each 100-m elevational band in metres | | MAT | Mean annual temperature (bio1) of each 100-m elevational band in °C | | TSE | Temperature seasonality (bio4) of each 100-m elevational band in °C/100 | | MAP | Mean annual precipitation (bio12) of each 100-m elevational band in kg m^-2 yr^-1 | | PSE | Precipitation seasonality (bio15) of each 100-m elevational band in kg m^-2 | | NPP | Net primary productivity (NPP) of each 100-m elevational band in g C m⁻² yr⁻¹ | | SOC | Soil organic carbon (SOC) of each 100-m elevational band in dg/kg (= 10 × g/kg) | | AET | Actual evapotranspiration (AET) of each 100-m elevational band in mm | | PET | Potential evapotranspiration (PET) of each 100-m elevational band in mm | | EHM | EVI homogeneity (EHM) of each 100-m elevational band | | TRI | Terrain ruggedness index (TRI) of each 100-m elevational band in meters | | WDF | Water deficit (WDF) of each 100-m elevational band in mm |

Codebook for siteplantswcvp.csv

| Column | Description | |-----------|-------------------------------------------------------------------| | taxonname | Accepted botanical names standardised according to World Checklist of Vascular Plants (WCVP) | | taxonauthors | Accepted botanical authorship standardised according to World Checklist of Vascular Plants (WCVP) | | genus | Accepted botanical genus epithet standardised according to World Checklist of Vascular Plants (WCVP) | | family | Accepted family of plant species standardised according to World Checklist of Vascular Plants (WCVP), which follows Angiosperm Phylogeny Group (APG) classification | | powodist | Distribution status (Introduced vs. Native) of plant according to World Checklist of Vascular Plants (WCVP) | | lifeformdescription | Lifeform description of selected plant species according to World Checklist of Vascular Plants (WCVP) | | climate_description | Climate description of selected plant species according to World Checklist of Vascular Plants (WCVP) | | Morni | Short for Morni Hills | | Chail | Short for Chail Wildlife Sanctuary | | Churdhar | Short for Churdhar Wildlife Sanctuary |

Codebook for sitespecelev.csv

| Column | Description | |-----------|-------------------------------------------------------------------| | taxon_name | Accepted botanical names standardised according to World Checklist of Vascular Plants (WCVP) | | LL | Lower elevational limit (in meters) of the species in Himalayas | | UL | Upper elevational limit (in meters) of the species in Himalayas |

Codebook for topmodcomparison.csv

| Column | Description | |---------|-------------------------------------------------------------------| | Site | Name of site for which the model was compared | | Model | Species richness model in y ~ x form | | logLik | log-likelihood of the model | | AICc | corrected Akaike's Information Criteria | | daicc | difference in corrected Akaike's Information Criteria from the top model | | dev.adj | adjusted deviance-squared for model |

References

• Amatulli, G., Domisch, S., Tuanmu, M.-N., Parmentier, B., Ranipeta, A., Malczyk, J., & Jetz, W. (2018). A suite of global, cross-scale topographic variables for environmental and biodiversity modeling. Scientific Data, 5, 180040. https://doi.org/10.1038/sdata.2018.40

• Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37(12), 4302–4315. https://doi.org/10.1002/joc.5086

• Govaerts, R., Lughadha, E. N., Black, N., Turner, R., & Paton, A. (2021). The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Scientific Data, 8(1), 215. https://doi.org/10.1038/s41597-021-00997-6

• Hengl, T., Jesus, J. M. de, Heuvelink, G. B. M., Gonzalez, M. R., Kilibarda, M., Blagotić, A., Shangguan, W., Wright, M. N., Geng, X., Bauer-Marschallinger, B., Guevara, M. A., Vargas, R., MacMillan, R. A., Batjes, N. H., Leenaars, J. G. B., Ribeiro, E., Wheeler, I., Mantel, S., & Kempen, B. (2017). SoilGrids250m: Global gridded soil information based on machine learning. PLoS ONE, 12(2), e0169748. https://doi.org/10.1371/journal.pone.0169748

• ICIMOD (2008). Outline Boundary of Hindu Kush Himalayan (HKH) Region. http://rds.icimod.org/

• Karger, D. N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R. W., Zimmermann, N. E., Linder, H. P., & Kessler, M. (2017). Climatologies at high resolution for the earth’s land surface areas. Scientific Data, 4, 170122. https://doi.org/10.1038/sdata.2017.122

• Rana, S. K., Price, T. D., & Qian, H. (2019). Plant species richness across the Himalaya driven by evolutionary history and current climate. Ecosphere, 10(11), e02945. https://doi.org/10.1002/ecs2.2945

• Rana, S. K., & Rawat, G. S. (2017). Database of Himalayan plants based on published floras during a century. Data, 2(4), 36. https://doi.org/10.3390/data2040036

• Rana, S. K., & Rawat, G. S. (2019). Database of vascular plants of Himalaya. Version 1.6. Dehradun: Wildlife Institute of India. https://doi.org/10.15468/zdeuix

• Trabucco, A., & Zomer, R. J. (2019). Global high-resolution soil-water balance (version 3). CGIAR Consortium for Spatial Information. https://doi.org/10.6084/m9.figshare.7707605.v3

• Tuanmu, M.-N., & Jetz, W. (2015). A global, remote sensing-based characterization of terrestrial habitat heterogeneity for biodiversity and ecosystem modelling. Global Ecology and Biogeography, 24(11), 1329–1339. https://doi.org/10.1111/geb.12365

• Zomer, R. J., Xu, J., & Trabucco, A. (2022). Version 3 of the global aridity index and potential evapotranspiration database. Scientific Data, 9, 409. https://doi.org/10.1038/s41597-022-01493-1

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